BN0855 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 5.5308e-07 2.8062e-05
Layer 4 3.6014e-06 1.7052e-04
Layer 2 1.3475e-05 2.9260e-04
Layer 5 5.2966e-05 7.2422e-03
Layer 6 1.5709e-02 1.6514e-01
Layer 1 4.1365e-01 4.2056e-01
WM 9.9918e-01 5.3459e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
INA Expression Distribution
Gene Specificity Score (GSS)
INA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
INA Layer 3 3.0586 0.8591
SNX3 Layer 3 2.8223 0.8580
SCN1B Layer 3 3.6445 0.8569
PIN1 Layer 3 2.9863 0.8565
SLC25A4 Layer 4 2.9697 0.8562
NAT8L Layer 3 3.1934 0.8558
LMO4 Layer 3 3.2793 0.8558
KCNA2 Layer 3 2.9375 0.8556
DCLK1 Layer 4 3.1523 0.8539
NPTN Layer 2 3.2637 0.8537
ATP2B2 Layer 3 3.0586 0.8535
RCAN2 Layer 3 2.9922 0.8521
BEX5 Layer 3 3.0391 0.8520
RAB3A Layer 3 3.1191 0.8506
PRDX2 Layer 3 3.0000 0.8487
GABRA1 Layer 3 3.2500 0.8475
ATP5MF Layer 3 2.9336 0.8471
MEF2C Layer 4 3.1494 0.8470
CHCHD10 Layer 3 3.0059 0.8468
RNF11 Layer 3 2.9473 0.8460
CPLX1 Layer 3 3.3359 0.8458
C9orf16 Layer 3 3.2285 0.8456
SH3GL2 Layer 3 2.9473 0.8454
ATP5PO Layer 3 2.9531 0.8451
SNCB Layer 2 3.0527 0.8446
GABRD Layer 3 3.3145 0.8441
MICOS10 Layer 3 2.9609 0.8440
ATP2A2 Layer 3 3.0000 0.8438
ATP6V0E2 Layer 3 2.9160 0.8438
MOAP1 Layer 3 2.9082 0.8437
COX5A Layer 3 2.9609 0.8437
EIF4G2 Layer 3 2.9863 0.8434
KIF1A Layer 4 3.0156 0.8432
NSF Layer 3 3.0996 0.8432
PRKAR1B Layer 3 2.9277 0.8427
NDUFB9 Layer 3 3.1602 0.8419
PARK7 Layer 3 3.0225 0.8415
SULT4A1 Layer 4 2.8906 0.8415
GOT1 Layer 3 2.8594 0.8414
SNAP91 Layer 3 2.9531 0.8414
SOD2 Layer 3 2.7793 0.8413
GABRB2 Layer 3 3.2578 0.8413
PGK1 Layer 3 2.9922 0.8410
HMGB1 Layer 4 2.9082 0.8409
CABP1 Layer 3 3.1055 0.8406
SV2A Layer 3 2.8457 0.8405
SNU13 Layer 4 2.8340 0.8404
EEF1B2 Layer 3 2.9531 0.8402
RETREG2 Layer 3 2.6777 0.8401
NDUFA1 Layer 3 2.8516 0.8396

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0855
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0855_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0855/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0855/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0855/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0855/report/PD/BN0855_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0855/report/PD/BN0855_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 01:43:54
  • Number of Processes: 10
  • Spending Time: 0h 3m